I recall reading your post on www.RoofingTalk.com
where you already received some advice, not at all being kind in any way to the contractor.
Firstly, in my opinion, he should be given an opportunity to make good on his promise to you that the items will be corrected as per your and his agreement to the punch-list items.
You see, just because someone makes mistakes, or their crew they hired to do the job does not make it look as nice as we all would expect, the true test is really more on if he is honest and ethical enough to attempt to do the right thing.
No, I do not think that the entire roof will need to be torn off.
Regarding some of those photos that you took from on top of the roof, would you notice the waviness of the rows from the front lawn?
Is so, they are necessitated to have straightened out.
Is there really missing flashings under the window sills, or did he just install the shingles over the top of the old existing sheet metal?
So, go at it like that first, before you crucify him and make your list and see what he is willing and capable of doing about those items first.
Then, gety back to us and report what his response is.
On the one exposed nail that I remember seeing this morning, there usually is one last piece of ridge cap shingle material that does have a face nail in it. Any exposed nails should be covered with a good quality caulking sealant of a similar color tone as the roof shingle color. Then that is fixed.
The cut ridge cap shingle where the ridge intersects with the main plane of the larger roof surface can be removed and replaced at a very minor inconvenience, but there usually does wind up being a slice in the shingle to conform to the pitch trasition change.
The wavy rows on the walk-on porch roof can be removed down to a course of shingles and then re-installed with chalk lines being snapped, to ensure that they are straight and true. A minor adjustment in the course exposure may need to be made, but rather than all at once, just around 1/8" to 1/4" per row, to make sure the shingles tie in to the steeper roof slope row correctly.
See if he will honor his commitment to providing you an adequate job.
Substantial completion and to conform to Industry Standards does not necessarily mean that the project will be perfect, but that it will work for the purpose intended.